Molecular data concerning the involvement of roots in the genetic pathways regulating floral transition are lacking. In this study, we performed global analyses of the root transcriptome in Arabidopsis in ... [more ▼]

Molecular data concerning the involvement of roots in the genetic pathways regulating floral transition are lacking. In this study, we performed global analyses of the root transcriptome in Arabidopsis in order to identify flowering time genes that are expressed in the roots and genes that are differentially expressed in the roots during the induction of flowering. Data mining of public microarray experiments uncovered that about 200 genes whose mutations are reported to alter flowering time are expressed in the roots (i.e. were detected in more than 50% of the microarrays). However, only a few flowering integrator genes passed the analysis cutoff. Comparison of root transcriptome in short days and during synchronized induction of flowering by a single 22-h long day revealed that 595 genes were differentially expressed. Enrichment analyses of differentially expressed genes in root tissues, gene ontology categories, and cis-regulatory elements converged towards sugar signaling. We concluded that roots are integrated in systemic signaling, whereby carbon supply coordinates growth at the whole plant level during the induction of flowering. This coordination could involve the root circadian clock and cytokinin biosynthesis as a feed forward loop towards the shoot. [less ▲]

Flowering is a hot topic in Plant Biology and important progress has been made in Arabidopsis thaliana toward unravelling the genetic networks involved. The increasing complexity and the explosion of ... [more ▼]

Flowering is a hot topic in Plant Biology and important progress has been made in Arabidopsis thaliana toward unravelling the genetic networks involved. The increasing complexity and the explosion of literature however require development of new tools for information management and update. We therefore created an evolutive and interactive database of flowering time genes, named FLOR-ID (Flowering-Interactive Database), that is available freely at http://www.flor-id.org. The hand-curated database contains information on 306 genes and links to 1595 publications gathering the work of more than 4500 authors. Gene function and interactions within the flowering pathways were inferred from the analysis of related publications, included in the database and translated into interactive manually drawn snapshots. [less ▲]

Flowering is a crucial step in plant development that needs to be carefully regulated to occur at the right time of the year, thus ensuring reproductive success. In Arabidopsis thaliana, several ... [more ▼]

Flowering is a crucial step in plant development that needs to be carefully regulated to occur at the right time of the year, thus ensuring reproductive success. In Arabidopsis thaliana, several interconnected molecular networks have been disclosed that mediate flowering response to environmental cues, such as photoperiod and temperature, or to endogenous factors, such as plant age or hormones. Many of these signalling pathways are systemic, i.e. involve regulatory mechanisms distant from the shoot apical meristem where floral transition eventually occurs. However, most investigations were focused on the aerial parts of the plant but ignored the roots. The aim of this Ph.D. thesis was to integrate the roots into a comprehensive overview of the genetic control of flowering in Arabidopsis. A prerequisite was to obtain a full list of known flowering-time genes. This step led to the creation of a database of flowering-time genes, which is accessible online and in which users can navigate through data tables or interactive schemes (www.flor-id.org). In the second part of the work, we studied the involvement of the roots in the differential developmental rates of plants grown in hydroponics and on soil. In the third part of the work, we used data mining analyses to show that about 200 flowering-time genes are expressed in the roots of Arabidopsis. Using a complementary approach, we analysed the root transcriptome to identify early changes occurring during the induction of flowering by a photoperiodic treatment. Collectively, the results presented in this work brought new insights in the regulation of flowering time at the whole-organism scale by integrating the “hidden part” of plants in the current landscape of the molecular processes controlling phase transitions in Arabidopsis thaliana. [less ▲]

Plant-based biopharmaceuticals have gained a lot of interest in the past decade due to their reduced cost and relative safety compared to mammalian cell cultures. While the first plant-made recombinant ... [more ▼]

Plant-based biopharmaceuticals have gained a lot of interest in the past decade due to their reduced cost and relative safety compared to mammalian cell cultures. While the first plant-made recombinant proteins are now reaching the market, the production systems still need improvements to maximize their competitiveness, proteolysis being one of the main factors limiting the yields. Identifying and inhibiting in vivo endogenous proteases involved in the degradation of recombinant proteins could then lead to a significant increase in production yields. In this study, we focused on two different production systems in Arabidopsis thaliana: rhizosecretion and cell suspensions. Extracellular proteases of both systems were used in vitro to study the conditions of target protein degradation (Bovine Serum Albumine, BSA). First, proteases from both systems degrade BSA at both acidic and neutral-to-basic pH conditions. Then, serine and metallopeptidases were shown to be the main protease classes responsible for BSA degradation by rhizosecreted proteomes or extracellular cell culture media, respectively. Finally, the biochemical tests were coupled to a bioinformatics analysis of publicly available transcriptomic data, in order to reduce the number of the proteases most likely involved in BSA degradation. Using this method, only five serine proteases and two metallopeptidases remain candidates for an amiRNA-mediated in vivo inhibition. [less ▲]

The transition to flowering is an essential step of the plant life cycle that is tightly controlled by both endogenous and environmental cues. Its regulation is extremely complex and involves hundreds of ... [more ▼]

The transition to flowering is an essential step of the plant life cycle that is tightly controlled by both endogenous and environmental cues. Its regulation is extremely complex and involves hundreds of genes that are part of highly interconnected pathways. Our knowledge of the molecular mechanisms governing the floral induction of Arabidopsis thaliana increases quickly and a significant number of reviews are published every year on this topic. However, most of them focus on a single pathway without highlighting the interconnections existing between them. Furthermore, those reviews become rapidly outdated, since our comprehension of the genetic control of flowering time evolves continuously. Hence, we believe that the current landscape of flowering time research in Arabidopsis misses an exhaustive repository of the genes involved in the control of flowering and their regulatory pathways. Here, we present a new interactive resource built around a curated database of the flowering time genes that brings together multiple pieces of information such as their function, the flowering time phenotype of mutants and overexpressing lines, the related key publications, etc. Our website thus gives access to a curated and exhaustive list of the genes involved in the regulation of flowering time in Arabidopsis as well as the regulatory pathways controlling their expression. Because of its flexibility, the database is highly dynamic and will be periodically updated with the future breakthroughs in this domain. [less ▲]

Vernalization establishes a memory of winter that must be maintained for weeks or months in order to promote flowering the following spring. The stability of the vernalized state varies among plant ... [more ▼]

Vernalization establishes a memory of winter that must be maintained for weeks or months in order to promote flowering the following spring. The stability of the vernalized state varies among plant species and depends on the duration of cold exposure. In Arabidopsis thaliana, winter leads to epigenetic silencing of the floral repressor gene FLOWERING LOCUS C (FLC) and the duration of cold is measured through the dynamics of chromatin modifications during and after cold. The growing conditions encountered post-vernalization are thus critical for the maintenance of the vernalized state. We reported that high temperature leads to devernalization and, consistently, to FLC reactivation in Arabidopsis seedlings. Here we show that the repressive epigenetic mark H3K27me3 decreases at the FLC locus when vernalized seedlings are grown at 30°C, unless they were first exposed to a stabilizing period at 20°C. Ambient temperature thus controls the epigenetic memory of winter. [less ▲]

Plant-based recombinant protein production systems have gained an extensive interest over the past few years, because of their reduced cost and relative safety. Although the first products are now ... [more ▼]

Plant-based recombinant protein production systems have gained an extensive interest over the past few years, because of their reduced cost and relative safety. Although the first products are now reaching the market, progress are still needed to improve plant hosts and strategies for biopharming. Targeting recombinant proteins toward the extracellular space offers several advantages in terms of protein folding and purification, but degradation events are observed, due to endogenous peptidases. This paper focuses on the analysis of extracellular proteolytic activities in two production systems: cell cultures and root-secretion (rhizosecretion), in Arabidopsis thaliana and Nicotiana tabacum. Proteolytic activities of extracellular proteomes (secretomes) were evaluated in vitro against two substrate proteins: bovine serum albumin (BSA) and human serum immunoglobulins G (hIgGs). Both targets were found to be degraded by the secretomes, BSA being more prone to proteolysis than hIgGs. The analysis of the proteolysis pH-dependence showed that target degradation was mainly dependent upon the production system: rhizosecretomes contained more peptidase activity than extracellular medium of cell suspensions, whereas variations due to plant species were smaller. Using class-specific peptidase inhibitors, serine and metallopeptidases were found to be responsible for degradation of both substrates. An in-depth in silico analysis of genomic and transcriptomic data from Arabidopsis was then performed and led to the identification of a limited number of serine and metallo-peptidases that are consistently expressed in both production systems. These peptidases should be prime candidates for further improvement of plant hosts by targeted silencing. [less ▲]

Flowering is a crucial step in plant life cycle and is therefore tightly controlled by both environmental and endogenous cues. The involvement of the aerial organs of the plant in the molecular mechanisms ... [more ▼]

Flowering is a crucial step in plant life cycle and is therefore tightly controlled by both environmental and endogenous cues. The involvement of the aerial organs of the plant in the molecular mechanisms controlling floral transition has been extensively documented while the participation of the roots remains poorly investigated. However, the induction of flowering by photoperiod involves systemic signals that move in the phloem from leaves to sinks, and hence presumably reach the roots. We therefore performed a transcriptomic analysis of the roots during the induction of flowering in Arabidopsis thaliana and indeed identified a large number of differentially expressed genes. A reverse genetic approach further confirmed the pleiotropic effects of flowering time genes on root architecture. [less ▲]

Flowering is one of the most important developmental steps in plant life cycle and is therefore tightly controlled by environmental cues. The involvement of the aerial part of the plant in the molecular ... [more ▼]

Flowering is one of the most important developmental steps in plant life cycle and is therefore tightly controlled by environmental cues. The involvement of the aerial part of the plant in the molecular mechanisms leading to floral transition is well documented while participation of the roots received less attention. Nevertheless, the induction of flowering by photoperiod is known to involve systemic signals that move in phloem sap towards sinks, throughout the plants, including the roots. Transcriptomic analysis of roots tissues during the floral induction of flowering by a single long day of in Arabidopsis thaliana by a single long day allowed us to identify a large number of differentially expressed genes. How mutations We subsequently selected in some candidate genes affect plant development - including root architecture and flowering time - is being to analyze their flowering timefurther analyzed. Further analysis of those genes will permit us to unravel their role in the flowering induction process. [less ▲]

Hydroponics and soil are the most common media used for plant growth. Hydroponics has the main advantage of providing easy access to the root system and is therefore commonly used for gene expression ... [more ▼]

Hydroponics and soil are the most common media used for plant growth. Hydroponics has the main advantage of providing easy access to the root system and is therefore commonly used for gene expression analyses in molecular studies of the model plant Arabidopsis thaliana. However, the impact of root substrate on plant growth remains poorly documented. Here we show that hydroponics accelerates both shoot growth and developmental phases as compared with culture on soil. In order to identify molecular changes in the roots that could account for these medium effects, a transcriptomic comparison was performed by microarray analysis. This experiment revealed that more than 20% of the genes were differentially expressed in hydroponics vs soil. Among them, the flowering time gene FLOWERING LOCUS C and two clades of microRNA targeted genes. To further assess the role of these genes in roots, artificial microRNAs were designed for root specific expression in transgenic Arabidopsis plants. [less ▲]

The metabolic roles of volatile organic compounds (VOCs) emitted by plant growth-promoting rhizobacteria (PGPR) and the identity of the molecules responsible for the growth promotion are still poorly ... [more ▼]

The metabolic roles of volatile organic compounds (VOCs) emitted by plant growth-promoting rhizobacteria (PGPR) and the identity of the molecules responsible for the growth promotion are still poorly documented. As well, the implication of microRNAs in root development is a recent discovery that deserves to be explored. In this study, the implication of microRNAs in the response of Brachypodium distachyon (L.) Beauv. Bd21 root architecture to rhizobacterial VOCs was investigated. Nineteen PGPR strains were screened to select those showing the strongest phenotypic effects. The strain Bacillus subtilis AP305-GB03 induced the most important promotion of biomass production and root development. Total RNA extraction and RT-qPCR analysis of microRNAs were performed on Bd21 root samples. The expression of miR160 a-d, miR164 f, miR167 c-d, miR397 b and miR399 a-b was measured in roots every 2 days during the first 10 days of Bd21 development, in the presence or absence of the bacterial VOCs. Differences in the expression profile of miR164 f and miR167 c-d were observed in the roots exposed to GB03 VOCs, as compared to the control. These differences could be correlated to the root system architecture modifications observed after 10 days of growth with GB03. miR397 b and miR399 a-b also showed differences in the expression profile of roots exposed to the bacterial VOCs. These microRNAs have been respectively involved in cold stress tolerance and in the response to phosphate starvation. [less ▲]

Root chicory (Cichorium intybus var. sativum) is a biennial crop, but is harvested for root inulin at the end of the first growing season before flowering. However, cold temperatures might vernalize seeds ... [more ▼]

Root chicory (Cichorium intybus var. sativum) is a biennial crop, but is harvested for root inulin at the end of the first growing season before flowering. However, cold temperatures might vernalize seeds or plantlets, leading to incidental early flowering and hence understanding the molecular basis of vernalization is important. A MADS-box sequence was isolated by RT-PCR and named FLC-LIKE1 (CiFL1) because of its phylogenetic positioning within the same clade as the floral repressor Arabidopsis FLOWERING LOCUS C (AtFLC). Moreover, overexpression of CiFL1 in Arabidopsis caused late flowering and prevented up-regulation of the AtFLC target FLOWERING LOCUS T gene by photoperiod, suggesting functional conservation between root chicory and Arabidopsis. Like AtFLC in Arabidopsis, CiFL1 was repressed during vernalization of seeds or plantlets of chicory, but repression of CiFL1 was unstable whether the post-vernalization temperature was favorable to flowering or whether it devernalized the plants. Instability of CiFL1 repression might be linked to bienniality of root chicory versus the annual life cycle of Arabidopsis. However, reactivation of AtFLC was also observed in Arabidopsis when a high temperature treatment was given straight after seed vernalization, erasing the promotive effect of cold on flowering. Cold-induced downregulation of a MADS-box floral repressor and its reactivation by high temperature thus appear as conserved features of the vernalization and devernalization responses in distant species.This article is protected by copyright. All rights reserved. [less ▲]

Cytokinins (CKs) are involved in many physiological processes. We observed that the application of N6-benzylaminopurine (BAP) to the roots of hydroponically grown plants of Arabidopsis thaliana promotes ... [more ▼]

Cytokinins (CKs) are involved in many physiological processes. We observed that the application of N6-benzylaminopurine (BAP) to the roots of hydroponically grown plants of Arabidopsis thaliana promotes flowering in non-inductive short days. The response to BAP treatment does no require FLOWERING LOCUS T (FT), but activates its paralogue TWIN SISTER OF FT (TSF), as well as FD and SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1) (D'Aloia et al., 2011). We present here complementary data obtained with transgenic plants overexpressing a catalytic CK OXIDASE/DEHYDROGENASE (CKX) in the roots. The high efficiency of BAP in promoting flowering in our experimental system contrasts with the variability that emerges from studies gathered in literature. Many factors, either experimental or inherent to plant material, might explain these discrepancies and we are interested in identifying endogenous regulators that might provide a mechanistic explanation. We are therefore investigating whether the endogenous pathways underlying plant developmental phase changes might regulate the relative contribution of CKs to flowering. [less ▲]

Cytokinins are involved in many aspects of plant growth and development and physiological evidence also indicates that they have a role in floral transition. In order to integrate these phytohormones into ... [more ▼]

Cytokinins are involved in many aspects of plant growth and development and physiological evidence also indicates that they have a role in floral transition. In order to integrate these phytohormones into the current knowledge of genetically defined molecular pathways to flowering, we performed exogenous treatments of adult wild-type and mutant Arabidopsis plants and analysed the expression of candidate genes. We used a hydroponic system that enables synchronous growth and flowering of Arabidopsis and allows precise application of chemicals to the roots for defined periods of time. We show that application of N6-benzylaminopurine (BAP) promotes flowering of plants grown in non-inductive short days. The response to cytokinin treatment does not require FLOWERING LOCUS T (FT) but activates its paralogue TWIN SISTER OF FT (TSF), as well as FD, which encodes a partner protein of TSF, and the downstream gene SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Treatment of selected mutants confirmed that TSF and SOC1 are necessary for the flowering response to BAP while the activation cascade might partially act independently of FD. These experiments provide a mechanistic basis for the role of cytokinins in flowering and demonstrate that the redundant genes FT and TSF are differently regulated by distinct floral inducing signals. [less ▲]